All sample Questions 13A, 14, 15, 19, 13B, 14B, 16, 17

5'

(1) What end (5' or 3') of the molecule is here? (Circle the correct answer).

In which of the ribosomal sites, the A site, P site, and/or E site, would the following be found (discuss the site where tRNA is predominantly found)? A. A tRNA without an amino acid attached B. A tRNA with a polypeptide attached C. A tRNA with a single amino acid attached

A. E site B. P site C. A site

Write out the mRNA sequences transcribed from the above normal and sickle cell DNA sequence

ACU CCU GAG GAG

Distinguish between an operon encoding a polycistronic message and a gene encoding a monocistronic message. Which is more likely to be observed in prokaryotic and which in eukaryotic cells?

Prokaryotes have polycistronic and eukaryotes have monocistronic messages.

Below are portions of the beta-globin gene sequence that codes for a normal hemoglobin and one that has the sickle cell mutation. Note that triplet codons are separated by a space. Normal DNA: Sickle Cell DNA: 5-ACT CCT GAG GAG -3' 3'-ACT CCT GTG GAG -5' 3'-TGA GGA CTC CTC-5' 3'- TGA GGA CAC CTC -5'

Questions

What does telomerase use for a template to make telomere repeat sequences?

RNA (in telomerase)

Make a list the similarities and differences between the function of RNA polymerase and DNA polymerase. (list at least 3 similarities and 2 differences)

RNA polymerase- dna template, synthesize 5' to 3' DNA polymerase- dna template, synthesize 5' to 3', primer, proofreads

What type of mutation is this? a. Nonsense b. Frameshift c. Missense d. Silent

C

Which of the following would not be found in a prokaryotic transcription complex? a. activator proteins bound to DNA b. repressor proteins bound to DNA c. mediator proteins activating RNA polymerase d. all of the above would not be found in a prokaryotic transcription complex e. all of the above would be found in a prokaryotic transcription complex

C

Which stage of protein synthesis is defined by the release of a polypeptide chain when a STOP codon is read by the ribosome? a) Propagation b) Elongation c) Termination d) Initiation

C

Which type of structure is formed when hydrophobic interactions occur between the peptides of amino acid chains? a.) Primary b.) Secondary c.) Tertiary d.) Quaternary

C

What is the function of a gene promoter? A. To regulate the rate of transcription B. To regulate the rate of translation C. To provide a starting point for transcription D. To provide a starting point for translation

d

1. The inclusion of his- mutant Salmonella in the AMES assay is required for: a. source of metabolite missing by auxotrophs b. source of test organism unable to grow in absence of histidine c. source of test organism sensitive to chemically induced DNA mutations d. a & b e. b&c

e.

Compare gene promoters in eukaryotic or prokaryotic cells. Name one similarity and one difference between them.

eukaryotes- core promotor, distant regulatory regions which means enhancers/activators and silencers/inhibitors are about 10,000 bp away prokaryotes- core promotor, close regulatory regions

TF) Mismatch repair involves several proteins that recognize and bind to bulky thymine dimers.

false

Describe the Ames test and how results are interpreted

his-auxotroph will mutate to wild type. If exposed to mutagen will then grow on media without his. If you see growth on a media without his means that you have a mutation caused by a putative mutagen

Describe the basic structure of normal adult hemoglobin and the abnormality observed in sickle-cell hemoglobin. What gene mutation causes the structural abnormality?

missense/base substitute change nucleotide>change aa Hb-B wild type will have a glutamic acid at proton 6, but with sickle mutation it will change to a valine glutamic acid is hydrophilic while valine is hydrophobic so it will fold inside which structure/function change will occur

The process of error correction of mismatched bases carried out by DNA polymerases is called__________.

proofreading

What type of DNA repair occurs during S-phase?___________, __________________

proofreading, mismatch repair (MMR)

During the initiation phase of translation, which ribosomal subunit binds specifically to mRNA?

small ribosomal subunit

What amino acids are encoded by these mRNA sequences (use the codon chart).

thr-pro-glu-glu

Write a brief description of the mutagenic action of the following mutagens: 5'bromouracil, acridine orange, ultraviolet light. Which would result in frameshift mutations

5'bromouracil-Box analog (t), acts like a C so it will bind a T-G mutation but doesn't occur to second round of replication but it will be fixed into the chromosome. acridine orange-intercalates(wedge) so polymerase slips which means frameshifts from inserts and deletions UV light-5 dimers must exercise (NER) which is called (XP) in humans

Look at the drawing below: ——————————————DNA polymerase-> ——————————————————————————— The line on the bottom represents the template strand, and the line on the top represents the strand that is being synthesized by DNA polymerase in the direction shown by the arrowhead. Label the 5' and 3' ends of the top and bottom strands

5'——————————————DNA polymerase->3' 3'———————————————————————————5'

If a eukaryotic chromosome has 25 origins of replication, how many replication forks does it have at the beginning of DNA replication?

50

How many times would telomerase have to bind to the end of the telomere in order to make a segment of DNA that is 36 nucleotides in length?

6 times

How many different sequences of mRNA could encode a peptide with the sequence alanine-glycine-methionine-serine? (Check the codon table to find the number of codons that specify each amino acid)

96 possible codons

1. A defect in DNA repair that occurs in families with Xeroderma pigmentosum A. Nucleotide excision repair B. Base excision repair C. DNA polymerase III proofreading D.recombination repair

A

What is the function of a gene promoter? A. To regulate the rate of transcription B. To regulate the rate of translation C. To provide a starting point for transcription D. To provide a starting point for translation

A

What is the genetic code? A. The relationship between a three-base codon sequence and an amino acid B. The entire base sequence of an mRNA molecule C. The entire sequence from the promoter to the terminator of a gene D. The binding of tRNA to mRNA

A

What type of protein structure is defined simply by peptide bonds between single amino acids? a.) Primary b.) Secondary c.) Tertiary d.) Quaternary

A

Explain how bacteria benefit by regulating the lac operon with a repressor protein and with an activator protein?

Available lactose will bind lac repressor to free the promotor to activate the proteins. When lactose is available it will "de repress" + allow polycistronic mRNA to be made which means proteins z, y, and a will be made. Freeing the promotor will increase the expression. The benefit is that you do not make unnecessary proteins in absence of lactose.

1. Let's suppose a mutation changed the third codon in the coding sequence of a gene into a stop codon. This would cause A. transcription to end too early. B. translation to end too early. C. transcription to end too late. bothAand B

B

1. The inclusion of liver extracts with the mutagen treatment of the his- auxotrophs in an AMES assay is required for: A. source of metabolite missing by auxotrophs B. source of enzymes required to activate mutagen C. source of human cells for testing carcinogens D. source of control for mutagen assay E.not required, but helpful

B

A tRNA has two major functional sites, which are A. 3' end where the amino acid binds and the codon sequence. B. 3' end where the amino acid binds and the anticodon sequence. C. the anticodon and the ribosome binding sequence. D. the codon and the ribosome binding sequence.

B

Assume a gene is under positive control and a small effector molecule causes the gene to be expressed at high levels. Which of the following mechanism could explain the action of this small effector molecule? A. It is an inhibitor that causes an activator protein not to bind to the DNA. B. It is an inducer that causes an activator protein to bind to the DNA. C. It is an inducer that causes a repressor to bind to the DNA. D. It is a corepressor that causes a repressor to not bind to the DNA.

B

What is an operon? A. A site in the DNA where a regulatory protein binds B. A group of genes under the control of a single promoter C. An mRNA that encodes several genes D. All of the above

B

What type of protein structure is defined by beta-pleated sheets and alpha helices? a.) Primary b.) Secondary c.) Tertiary d.) Quaternary

B

When an E. coli cell is exposed to lactose, how does this affect the regulation of the lac operon via lac repressor? A. the lac repressor binds to the operator and transcription is increased. B. the lac repressor does not bind to the operator and transcription is increased. C. the lac repressor binds to the operator and transcription is decreased. D.the lac repressor does not bind to the operator and transcription is decreased

B

Which of following types of genetic sequences would come first in a gene? A. Start codon B. Promoter C. Terminator D. Ribosome-binding sequence

B

Which of the following categories of mutations are not possible to pass to offspring? A. silent B. somatic C. frameshift D. induced E. X-linked

B

Which of the following statements about the spliceosome is false? A. A spliceosome splices pre-mRNA molecules. B. A spliceosome removes exons from RNA molecules. C. A spliceosome is composed of snRNPs. D. A spliceosome recognizes the exon-intron boundaries and the branch site.

B

One of the following statements about DNA replication is false. Circle the false statement below. A. A DNA double helix obeys the AT/GC rule. B. A DNA double helix could contain one strand that is 4 generations older than its complementary strand. C. A DNA double helix may contain two strands of DNA that were made at the same time. D. A DNA strand can serve as a template strand on many occasions. E. Following semiconservative DNA replication, one strand is a newly made daughter strand and the other strand is a parental strand.

C

The function of aminoacyl-tRNA-synthetase is to A. promote the binding of a tRNA to an mRNA. B. catalyze peptide bond formation between an incoming amino acid and a polypeptide. C. attach an amino acid to a tRNA. causetheinitiator tRNA tobindtothesmall ribosomal subunit

C, 20 specific tRNA or 20 amino acids

A - B - C - D - E - F - G - H - I - J - K - L A substitution of Adenine for Cytosine in the 7th base in the coding region of the mRNA (counting from the 5' end of the coding region of the mRNA).

Change codon J

96. Which of the following categories of mutations may not demonstrate a phenotype? A. Degenerate codon mutations (at wobble position) B. Neutral mutations (no significant change in structure/function) C. Mutation in unimportant region of protein D. All of the above E.None of the above

D

During homologous recombination repair which of the following occur? a) a Holliday junction forms b) branch migration occurs. c) A heteroduplex region forms d)All of the above occur

D

Which of the following properties of DNA polymerase is/are the reason(s) why it cannot synthesize the tips of eukaryotic chromosomes? A. It requires a primer to begin synthesis. B. It cannot synthesize DNA in the 3' to 5' direction. C. It cannot synthesize DNA in the 5' to 3' direction. D. Both A and B are correct.

D

Which of the following statements is false? A. The leading strand is made in the same direction that the replication fork is moving. B. The leading strand needs a primer at the origin of replication. C. The lagging strand is made in Okazaki fragments. D. The leading strand is synthesized in the 5' to 3' direction, while the lagging strand is synthesized in the 3' to 5' direction.

D

The Ames test detects A. DNA B. RNA C. proteins D. mutagens E. carcinogens

D

The proofreading function of DNA polymerase involves the recognition of a ________ and the removal of a short segment of DNA in the __________ direction. A. missing base, 5′ to 3′ B. base pair mismatch, 5′ to 3′ C. missing base, 3′ to 5′ D. base pair mismatch, 3′ to 5

D

The reading frame begins with a _____________ and is read ___________________. A. promoter, one base at a time B. promoter, in groups of three bases C. start codon, one base at a time D. start codon, in groups of three bases

D

Which class of mutations results in a series of multiple amino acid changes in proteins, often resulting in a premature stop codon (downstream of the mutation site)? A.base analogue B.transversion C.transition D.frameshift E.recombinant

D

Which of the following can result in base substitutions? A. alkylating agent B. base analogs C. Radiation All of the above

D

Which of the following is/are a common modification that happens to mRNA in complex eukaryotes such as humans? A. Splicing B. Attachment of a 5'-cap C. Attachment of a polyA tail D. All of the above

D

TF) Certain base analogues such as 5-bromouracil causes mutations by chemically altering nitrogenous bases in non-replicating DNA.

False

Phenylketonuria is a recessive metabolic disease which is caused by the absence of the enzyme phenylalanine hydroxylase. What is the phenotype of the disease and what causes the phenotype to develop? (hint what metabolic intermediate builds up?)

Foul to process of phenylalanine (phe). Increase phe which causes mental retardation. increase in phe but decrease in tyrosine

A - B - C - D - E - F - G - H - I - J - K - L An insertion of a base between the 9th and 10th positions of the coding region of the mRNA (counting from the 5' end of the coding region of the mRNA).

Frameshift mutation

How will the altered amino acid in the sickle cell globin affect folding of the protein? (Hint: compare their classification as hydrophobic or hydrophilic amino acids)

Hydrophilic glu > hd val fold ab so sticky so leuphin form and contort RBC (packed full with HB-B)

lagging

Is this strand the leading or lagging strand? (Circle the correct answer)

Part 2. Given that most antibiotics work by inhibiting translation and are not toxic to human cells, can you explain why antibiotics are generally not toxic to humans?

It has no effect on Eukaryotic translation but it can track bacterial infection caused by prokaryotes

Why is ATP is needed to attach an amino acid to a tRNA molecule?

It is just for an energy source to break bonds and make new ones

A - B - C - D - E - F - G - H - I - J - K - L Let's suppose that a mutation changes a sense codon within the middle of the coding sequence of a protein-encoding gene into a stop codon. How would this mutation affect transcription and translation?

Nonsense mutation so stops translocated protein

An mRNA has the sequence, 5'-AUGCCGUACCUAGC-3'. Write out the sequence of the coding and template strands of the DNA that encodes this mRNA and indicate the 5' and 3'ends. Does RNA polymerase slide along the template strand in the 5' to 3' direction or in the 3' to 5' direction?

Only adds to 3' hydroxyl

What is the wobble hypothesis?

The 3rd position of the codon is flexible and can vary via wobbling and the same tRNA can bind to two different codons

Given below is a hypothetical "wild type" polypeptide containing twelve amino acids (each letter arbitrarily represents one amino acid) A - B - C - D - E - F - G - H - I - J - K - L

The amino acid "A" is at the C (carboxyl) terminus and amino acid "L" is at the N (amino) terminus. Label the two ends of the molecule with -COOH or -NH3. Then modify the peptide sequence (based on mutations described below) and write it down under each of the statements below (use an X to depict unknown amino acids).

3'

The letter A is nearest the 5' or 3' end of the molecule?

5'

The letter B is nearest the 5' or 3' end of the molecule?

3'

The letter C is nearest the 5' or 3' end of the tRNA molecule?

During DNA replication, what is the function of primase?

The source of the RNA primer. Synthesizes RNA primers

TF) DNA strand replication begins with an RNA primer

True

TF) In general, DNA replicates semiconservatively and bidirectionally.

True

TF) When a metabolic block occurs in a biochemical pathway, it is common for the substance immediately prior to that block to accumulate in amount .

True

rna primer

What nucleic acid is probably depicted here (dotted line)?

In-born errors in metabolism can be studied in the bread mold Neurospora. Auxotrophic mutants are unable to synthesize a key substance, so can only survive if media is supplemented with that substance. For example, Tryptophan auxotrophic mutants in Neurospora can be "cured" by culturing in medium containing Tryptophan. What other substances can permit their survival ?

Tryptophan is downstream but say argenine is upstream and there was a block from converting arg to tryptophan will build up arg. So that means people need to be supplemented with tryptophan in their diet. Another way to permit their survival is to say citruline to arg to tryptophan. Which means you can also give arg here if it CAN convert.

During translation, chain termination is signaled by which triplets?

UAA, UAG, UGA

Okazaki fragments

What are these short DNA fragments usually called?

5'

What end (5' or 3') of the molecule is here? (Circle the correct answer).

Helicase

What enzyme is probably functioning here to unwind the DNA?

ligase

What enzyme probably functions here to couple these two newly synthesized fragments of DNA?

N

Which terminus (N or C) of the growing polypeptide chain is nearest the letter E?

A class of DNA polymerases called "translesion-replicating polymerases" have a flexible active site that allows replication of aberrant template strand. An advantage of translesion-replicating polymerases is that they can replicate____________, but a disadvantage is that they _____________ a. very quickly, have low fidelity b. over damaged DNA, have low fidelity c. when resources are limited, are very slow d. over damaged DNA, are very slow

b

Which of following types of genetic sequences would come first in a gene? A. Start codon B. Promoter C. Terminator D.Ribosome-binding sequence

b

Can SOMATIC autosomal dominant mutations have any effect on a population? __ on an individual carrying them? ___ A. No, No B. Yes, No C. No, Yes D.Yes,Yes

c